BioC 3.5: CHECK report for synapter on oaxaca

Package: synapter

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synapter_1.17.0.tar.gz

StartedAt: 2017-03-04 09:52:07 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:56:04 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 237.8 seconds

RetCode: 0

Status:  OK

CheckDir: synapter.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synapter_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/synapter.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synapter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synapter’ version ‘1.17.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘synapter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateGridPerformance: no visible global function definition for
  ‘setNames’
doHDMSePredictions: no visible global function definition for ‘predict’
getQs: no visible global function definition for ‘quantile’
makeMaster : <anonymous>: no visible global function definition for
  ‘loess’
makeMaster : <anonymous>: no visible global function definition for
  ‘predict’
modelRetTime: no visible global function definition for ‘loess’
modelRetTime: no visible global function definition for ‘predict’
modelRetTime: no visible global function definition for ‘fitted’
plot.all.features: no visible global function definition for ‘par’
plot.all.features: no visible global function definition for ‘grid’
plot.some.features: no visible global function definition for ‘text’
plot.some.features: no visible global function definition for ‘grid’
plot.some.features: no visible global function definition for ‘points’
plot.some.features: no visible global function definition for ‘predict’
plot.some.features: no visible global function definition for ‘rect’
plot.some.features: no visible global function definition for ‘legend’
plotErrorPpm: no visible global function definition for ‘layout’
plotErrorPpm: no visible global function definition for ‘par’
plotErrorPpm: no visible global function definition for ‘hist’
plotErrorPpm: no visible global function definition for ‘rug’
plotErrorPpm: no visible global function definition for ‘legend’
plotErrorPpm: no visible global function definition for ‘lines’
plotErrorPpm: no visible global function definition for ‘density’
plotErrorPpm: no visible global function definition for ‘rnorm’
plotErrorPpm: no visible global function definition for ‘sd’
plotErrorPpm: no visible global function definition for ‘abline’
plotErrorPpm: no visible global function definition for ‘quantile’
plotErrorPpm: no visible global function definition for ‘boxplot’
plotLowess: no visible global function definition for ‘par’
plotLowess: no visible global function definition for ‘abline’
plotLowess: no visible global function definition for ‘grid’
plotLowess: no visible global function definition for ‘lowess’
plotLowess : <anonymous>: no visible global function definition for
  ‘lowess’
plotLowess : <anonymous>: no visible global function definition for
  ‘lines’
plotLowess: no visible global function definition for ‘legend’
plotLowess2: no visible global function definition for ‘grid’
plotLowess2: no visible global function definition for ‘polygon’
plotLowess2: no visible global function definition for ‘abline’
plotLowess2: no visible global function definition for ‘points’
plotLowess2: no visible global function definition for ‘lines’
plotLowess2: no visible global function definition for ‘fitted’
plotRetTimeDiffs: no visible global function definition for ‘fitted’
plotRetTimeDiffs: no visible global function definition for ‘hist’
plotRetTimeDiffs: no visible global function definition for ‘rug’
qPlot: no visible global function definition for ‘axis’
qPlot: no visible global function definition for ‘grid’
qPlot: no visible global function definition for ‘abline’
qPlot: no visible global function definition for ‘segments’
synergise: no visible global function definition for ‘tk_choose.dir’
synergise: no visible global function definition for ‘jpeg’
synergise: no visible global function definition for ‘dev.off’
synergise: no visible global function definition for ‘svg’
plot,MasterFdrResults-missing: no visible global function definition
  for ‘text’
plot,MasterFdrResults-missing: no visible global function definition
  for ‘abline’
plot,MasterFdrResults-missing: no visible global function definition
  for ‘points’
plotFdr,Synapter : .qplot: no visible global function definition for
  ‘quantile’
plotFdr,Synapter : .qplot: no visible global function definition for
  ‘lines’
plotFdr,Synapter : .qplot: no visible global function definition for
  ‘legend’
plotFdr,Synapter: no visible global function definition for ‘par’
plotPpmError,Synapter: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline axis boxplot density dev.off fitted grid hist jpeg layout
  legend lines loess lowess par points polygon predict quantile rect
  rnorm rug sd segments setNames svg text tk_choose.dir
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "svg")
  importFrom("graphics", "abline", "axis", "boxplot", "grid", "hist",
             "layout", "legend", "lines", "par", "points", "polygon",
             "rect", "rug", "segments", "text")
  importFrom("stats", "density", "fitted", "loess", "lowess", "predict",
             "quantile", "rnorm", "sd", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
synergise 7.383  0.480  12.305
Synapter  6.354  0.242   8.015
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/synapter.Rcheck/00check.log’
for details.

* installing *source* package ‘synapter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (synapter)

name	user	system	elapsed
MasterFdrResults-class	0.001	0.000	0.001
Synapter	6.354	0.242	8.015
synapterTinyData	0.159	0.012	0.172
synergise	7.383	0.480	12.305